Brian Osborne | 6 Aug 17:38 2006

FW: A bio-perl networking problem

------ Forwarded Message
From: deepak shingan <deep_ans <at>>
Date: Sun, 06 Aug 2006 01:09:42 -0700 (PDT)
To: <osborne1 <at>>
Subject: A bio-perl networking problem

Hello Sir, 
I am in a greate trouble and I really want your help.

I am using SearchIO algorithm for parsing the blast result file in the
xml-rpc environment.

I have a client and server written in perl. The very first request that
I am sending is getting executed and I am able to see the output result
at the client side.
But for the second request I am sending is not getting executed
succesfully. Even it dose not throw any exception.
I think the problem is with "->next_result" statement which can not collect
result on the second request even the file contains many hits.
Can you give some light on this. I am really sorry for disturbing you
but I am not  able to make out anything.
So please help me. 

Here , I am sending the source code for testClient and testParser and
also a tempoaray Blast result file for testing.


Thanks and egoursly waiting for your responce.
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Hilmar Lapp | 6 Aug 21:38 2006

Re: Bio::Species, Bio::Taxonomy::Node overhaul

Wow! This is quite a number of changes to digest. Thanks for the  
detailed documentation.

I have three comments.

1) It sounds a bit that you changed the behavior of get_lca() such  
that users may have to adjust their code? If this is true, then this  
needs to be made clear in the 1.6 release as that part will not be  
backward compatible. If this is not true, then why did you have to  
change the implementation of Bio::Tools::Phylo::PAML to make tests  
pass? I.e., to what extent can what broke Bio::Tools::Phylo::PAML  
also break someone's script?

2) I can't find object_id() on Tree::Node or Taxonomy::Taxon. Where  
is/was it? The reason I am asking is that this method is part of the  
Bio::IdentifiableI API and therefore if you want to deprecate it you  
are suggesting to deprecate implementing Bio::IdentifiableI, and the  
rest of those methods need to be deprecated along.

3) Your whole email should probably go on the wiki, linked somewhere  
under documentation or release notes. Or somebody has a better idea?


On Aug 5, 2006, at 12:42 PM, Sendu Bala wrote:

> After the initial round of changes to Taxonomy described at
> (now committed),
> further changes will allow for the transition of Bio::Species to
> Bio::Taxonomy::Node (renamed to Bio::Taxon), and for Taxon to be fully
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